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Racemic protein crystal structure of aureocin A53 from Staphylococcus aureus in the presence of citrate and acetate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2N8O 2N8O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 292 A racemic mixture of L-Aureocin A53 and D-Aureocin A53 at 40 mg/mL concentration was mixed 1:1 with 0.2 M ammonium acetate, 0.2 M sodium citrate and 29% PEG 4000 v/v precipitant condition, pH 5.6 in a 1 microlitre sitting drop. Crystals were submerged in 20% PEG 400 in the precipitant solution as cryoprotectant and flash frozen in liquid nitrogen during harvesting.
Crystal Properties Matthews coefficient Solvent content 3.23 61.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.07 α = 90 b = 37.28 β = 93.05 c = 113.95 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2019-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9119 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.21 36.48 96.6 0.998 8.8 3.1 90457
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.21 1.23 80.3 0.617 1 1.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2N8O 1.21 36.48 90456 4505 96.37 0.189 0.187 0.1919 0.2208 0.2229 20.282
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -1.514 0.138 0.371 1.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.688 r_dihedral_angle_3_deg 10.956 r_dihedral_angle_1_deg 5.012 r_lrange_it 3.258 r_lrange_other 2.916 r_scangle_it 2.427 r_scangle_other 2.426 r_scbond_it 2.068 r_scbond_other 2.067 r_mcangle_other 1.903
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.688 r_dihedral_angle_3_deg 10.956 r_dihedral_angle_1_deg 5.012 r_lrange_it 3.258 r_lrange_other 2.916 r_scangle_it 2.427 r_scangle_other 2.426 r_scbond_it 2.068 r_scbond_other 2.067 r_mcangle_other 1.903 r_mcangle_it 1.901 r_mcbond_it 1.596 r_mcbond_other 1.594 r_rigid_bond_restr 1.41 r_angle_refined_deg 1.339 r_angle_other_deg 1.263 r_nbd_other 0.302 r_nbd_refined 0.222 r_nbtor_refined 0.204 r_symmetry_nbd_refined 0.2 r_symmetry_nbd_other 0.166 r_xyhbond_nbd_refined 0.16 r_symmetry_xyhbond_nbd_refined 0.093 r_chiral_restr 0.081 r_symmetry_nbtor_other 0.078 r_symmetry_xyhbond_nbd_other 0.026 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1704 Nucleic Acid Atoms Solvent Atoms 387 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing Coot model building